In order to explore cell expression during muscle regeneration in young(2-3 months) and old(18-22 months) cells, RNAseq experiments were performed using cells sorted and FACs at four time points:
The cell types sampled were as follows:
The RNA-seq data is aligned to the GRCm38 genome with STAR and counted with FeatureCount .
Only transcripts associated with coding proteins are kept.
Differentially expressed genes (DEG) processed with DESeq2_1.30.1 old vs young (reference expression is young one), for each cell type at each time Day_TypeCell_Old vs Day_TypeCell_Young
GSEA on all genes. This analysis is done by day and cell type on list of genes ranked by logfoldchange sign * padj decreasing. The data base use is genes set from Molecular Signatures DataBase (MSigDB) species :
How many pathways are significants (padj<0.05)
| ECs | FAPs | MuSCs | Inflammatory-Mac | Neutrophils | Resolving-Mac | NumberPathwayEnrichedByDay | |
|---|---|---|---|---|---|---|---|
| D0 | 0 | 69 | 66 | NA | NA | NA | 103 |
| D2 | 0 | 82 | 382 | 1 | 3 | 10 | 396 |
| D4 | 125 | 4 | 284 | 2 | NA | 19 | 308 |
| D7 | 4 | 0 | 17 | NA | NA | 0 | 21 |
| NumberPathwayEnrichedByTypeCell | 126 | 108 | 466 | 3 | 3 | 29 |
All condition combined, there are 499 pathway enriched. In this representation only pathway with upper letter are enriched in at least one condition.
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| Numbers conditions enrichis | 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 |
|---|---|---|---|---|---|---|---|---|
| Numbers pathways | 240 | 121 | 52 | 31 | 29 | 22 | 3 | 1 |